Academica suffered a torrid return to European football after a 40-year absence as Viktoria Plzen swept aside any hopes of an upset with a 3-1 victory.
Academica, shock winners of the Portuguese Cup over Sporting Lisbon last season, had stunned their Czech hosts by taking the lead in the Strunc Park stadium through Wilson Eduardo in the Europa League Group B match and holding on until the break.
Plzen had enjoyed the lion's share of possession and chances, however, and that dominance finally told as they ran away with the match in the second half with goals from Pavel Horvath, Michal Duris and Frantisek Rajtoral.
Academica had withstood some early pressure before Eduardo scored with the visitors' first real opportunity of the match.
Young Guinean forward Salim Cisse broke down the left and the 19-year-old's cross was turned in by the 22-year-old Eduardo from close range.
Plzen hit the woodwork to increase home frustrations at the break but it was a different story in the second half.
Veteran skipper Horvath took only two minutes of the second period to bring the scores level with a header from Vladimir Darida's corner.
Just before the hour-mark, Slovakian forward Duris made it 2-1 with a powerful header at the near post from David Limbersky's ball.
Blond-haired winger Rajtoral wrapped it up for the home side with the third header of the match, nodding home Marek Hanousek's floated cross to secure the Czechs all three points.